def test_validation(self):
symm_group_1 = [ [1,2] ] # This is a single symm group. It means that atom 1 and 2 are equivalent. We will try
# to swap 1 and 2.
symm_group_2 = [ [3,4],[5,6] ] # This is a single symm group. It means that atom 3 and 4, as well as
# atoms 5,6 are equivalent, and they have to be swapped at the same time.
# We will try with the following combinations:
# (3,4) (5,6)
# (4,3) (6,5)
# The validation function validates a list of this symmetry groups. When we use this list, all permutations are
# used (i.e. sym_perm(symm_group_1) x sym_perm(symm_group_2)). That is:
# (1,2) (3,4) (5,6)
# (1,2) (4,3) (6,5)
# (2,1) (3,4) (5,6)
# (2,1) (4,3) (6,5)
# A symm group is not a valid description
self.assertRaises(ValueError, symm_groups_validation, symm_group_1)
# A list of symm groups is a valid symmetry descriptor
try:
symm_groups_validation([symm_group_1])
symm_groups_validation([symm_group_1, symm_group_2])
except ValueError:
self.fail("Value exception has been raised.")
symm_group_3 = [ [2,1,3] ] # A symm group must have elements of len 2
self.assertRaises(ValueError, symm_groups_validation, [symm_group_3])
def __init__(self,
calculatorType,
fittingCoordsets,
calculationCoordsets=None,
fitSymmetryGroups=[],
calcSymmetryGroups=[]):
"""
Class constructor.
@param calculatorType: One of the calculators returned by 'availableCalculators()'. i.e. KABSCH_OMP_CALCULATOR
@param fittingCoordsets: An array containing the used coordinates of each conformation. It has the following form:
coordsets: [Conformation 1, Conformation 2, ..., Conformation N]
Conformation: [Atom 1, Atom 2,..., Atom M]
Atom: [x,y,z]
This coordinates will be used for both structural superposition and RMSD calculation if the 'calculation
coordinates' parameter is not defined.
The array type is constrained to be a numpy.array object with dtype = numpy.float64 (dtype will not be always double
by default).
Input coordinates are modified after each operation (usually centered and superposed into reference conformation).
@param calculationCoordsets: An array containing the coordinates used to calculate the RMSD. Must have the same structure
than 'fittingCoordinates'.
@param fitSymmetryGroups: List of symmetry groups.
Symm. groups are a low-level structure-agnostic of the type of symmetries that can be found in some ligands,
i.e. in rotating benzene groups. It can also be used in symmetries of bigger selections though.
See :py:func:`pyRMSD.symmTools.symm_permutations`
@param calcSymmetryGroups: As in 'fitSymmetryGroups', a list of symmetry groups.
@author: vgil
@date: 26/11/2012
"""
if not calculatorType in availableCalculators():
print("Calculator ", calculatorType,
" is not an available calculator.")
raise ValueError
else:
self.fitting_coordinates = fittingCoordsets
self.calculator_type = calculatorType
self.number_of_conformations = self.fitting_coordinates.shape[0]
self.number_of_fitting_atoms = self.fitting_coordinates.shape[1]
self.calculation_coordinates = calculationCoordsets
if self.calculation_coordinates is not None:
self.calculation_coordinates = calculationCoordsets
if self.number_of_conformations != self.calculation_coordinates.shape[
0]:
print(
"Calculation coordinates must hold the same number of conformations than fitting coordinates."
)
raise ValueError
self.number_of_calculation_atoms = self.calculation_coordinates.shape[
1]
else:
self.number_of_calculation_atoms = 0
# Default values for openMP and CUDA flags
self.__threads_per_block = 32
self.__blocks_per_grid = 8
self.__number_of_threads = 8
# Symmetry group handling
symm_groups_validation(fitSymmetryGroups)
symm_groups_validation(calcSymmetryGroups)
self.fit_symmetry_groups = fitSymmetryGroups
self.calc_symmetry_groups = calcSymmetryGroups
def __init__(
self, calculatorType, fittingCoordsets, calculationCoordsets=None, fitSymmetryGroups=[], calcSymmetryGroups=[]
):
"""
Class constructor.
@param calculatorType: One of the calculators returned by 'availableCalculators()'. i.e. KABSCH_OMP_CALCULATOR
@param fittingCoordsets: An array containing the used coordinates of each conformation. It has the following form:
coordsets: [Conformation 1, Conformation 2, ..., Conformation N]
Conformation: [Atom 1, Atom 2,..., Atom M]
Atom: [x,y,z]
This coordinates will be used for both structural superposition and RMSD calculation if the 'calculation
coordinates' parameter is not defined.
The array type is constrained to be a numpy.array object with dtype = numpy.float64 (dtype will not be always double
by default).
Input coordinates are modified after each operation (usually centered and superposed into reference conformation).
@param calculationCoordsets: An array containing the coordinates used to calculate the RMSD. Must have the same structure
than 'fittingCoordinates'.
@param fitSymmetryGroups: List of symmetry groups.
Symm. groups are a low-level structure-agnostic of the type of symmetries that can be found in some ligands,
i.e. in rotating benzene groups. It can also be used in symmetries of bigger selections though.
See :py:func:`pyRMSD.symmTools.symm_permutations`
@param calcSymmetryGroups: As in 'fitSymmetryGroups', a list of symmetry groups.
@author: vgil
@date: 26/11/2012
"""
if not calculatorType in availableCalculators():
print "Calculator ", calculatorType, " is not an available calculator."
raise ValueError
else:
self.fitting_coordinates = fittingCoordsets
self.calculator_type = calculatorType
self.number_of_conformations = self.fitting_coordinates.shape[0]
self.number_of_fitting_atoms = self.fitting_coordinates.shape[1]
self.calculation_coordinates = calculationCoordsets
if self.calculation_coordinates is not None:
self.calculation_coordinates = calculationCoordsets
if self.number_of_conformations != self.calculation_coordinates.shape[0]:
print "Calculation coordinates must hold the same number of conformations than fitting coordinates."
raise ValueError
self.number_of_calculation_atoms = self.calculation_coordinates.shape[1]
else:
self.number_of_calculation_atoms = 0
# Default values for openMP and CUDA flags
self.__threads_per_block = 32
self.__blocks_per_grid = 8
self.__number_of_threads = 8
# Symmetry group handling
symm_groups_validation(fitSymmetryGroups)
symm_groups_validation(calcSymmetryGroups)
self.fit_symmetry_groups = fitSymmetryGroups
self.calc_symmetry_groups = calcSymmetryGroups